This is a implementation of High Dimensional Neural Network Potential(HDNNP) designed to reproduce Density Function Theory(DFT) calculation effectively with high flexibility, reactivity.
The more detailed docs https://hdnnp.readthedocs.io/en/latest/index.html
There is equivalent doc in Japanese README.ja.md.
Install this project by git
.
$ git clone https://github.com/ogura-edu/HDNNP.git
# or if using ssh
$ git clone git@github.com:ogura-edu/HDNNP.git
This project uses Pipenv for development workflow. If you don't have it, run this command to install.
macOS
$ brew install pipenv
other
# please run after installing python
$ pip install pipenv
Same as by anaconda, but you need to install python rather than installing anaconda.
This bug will be fixed in near future release(ref: pythonfinder + pyenv + anaconda issue).
Set environmental variable PIPENV_VENV_IN_PROJECT
to 1
to create your VM into this project dir(/path/to/HDNNP/.venv
).
export PIPENV_VENV_IN_PROJECT = 1
For macOS users, you need to install mpich
before installing dependencies.
# Only for macOS users.
#
# NOTE: Installing both mpich and openmpi will conflict
#
$ brew install mpich
# or
$ brew install openmpi
Setup your enviroments.
# Install dependencies
$ pipenv install --dev
# activate your VM
$ pipenv shell
# For example...
(HDNNP) $ hdnnpy training
# deactivate
(HDNNP) $ exit
Using anaconda is prefered because it is basically faster than Pipenv.
Install anaconda and activate your VM.
$ ANACONDA_VERSION = [YOUR_ANACODA_VERSION]
$ pyenv install $ANACONDA_VERSION
$ pyenv local $ANACONDA_VERSION
$ conda env create -n HDNNP --file condaenv.yaml
$ echo ". ${HOME}/.pyenv/versions/<anacondaVERSION>/etc/profile.d/conda.sh" > ~/.bashrc
# activate
$ conda activate HDNNP
# install this program using pip
(HDNNP) $ pip install --editable .
# For example...
(HDNNP) $ hdnnpy training
# deactivate
(HDNNP) $ conda deactivate
NOTE
There is no
- ChainerMN
- Chainer v5
on the Anaconda Cloud, so you still have to install these packages by pip
.
And these is a bug that if you install anaconda by pyenv
, pipenv
will fail to start(ref: pythonfinder + pyenv + anaconda issue).
- Jörg Behler. First Principle Neural Network Potentials for Reactive Simulations of Large Molecular and Condensed System, 2007